Identification of EGL-43 target genes in C. elegans L3 larvae.
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE144292 | GEO | 2020/03/09
REPOSITORIES: GEO
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Project description:Depending on the cellular context, TF expression can vary dramatically both spatially and temporally. These differences in expression patterns can result in tissue-specific differences in TF binding to downstream targets. To identify targets on a tissue-specific basis, Targeted DamID (TaDa) has been recently introduced to generate TF binding profiles in various models including C. elegans. However, TaDa suffers from portability such that a new promoter-TF fusion transgene must be constructed for every new experimental condition of interest. Here, we adapt NanoDam for usage in C. elegans, which relies on the use of endogenous TF-GFP knock-ins, a plethora of which have already been generated by the community. We report that NanoDam single copy transgenes consisting of lowly expressed, tissue-specific GFP nanobody-Dam fusions, when combined with endogenous GFP-tagged alleles of TFs, results in robust, tissue-specific profiling. Using an endogenous GFP-tagged allele of EGL-43/EVI1, we performed NanoDam profiling of two disparate tissue types, the anchor cell (AC) and dopaminergic neurons, and identify targets unique to each and shared by both cell types. We also identify two GATA TFs, ELT-6 and EGL-18, as novel regulators of AC invasion. Taken together, we demonstrate that NanoDam is capable of profiling endogenous GFP-tagged TFs to identify novel downstream targets in specific cell types of C. elegans.
2023-06-30 | GSE232946 | GEO
Project description:NanoDam Profiling of EGL-43 in the Anchor Cell
| PRJNA974461 | ENA
Project description:Identification of EGL-43 target genes in C. elegans L3 larvae.
| PRJNA603322 | ENA
Project description:NanoDam Profiling of EGL-43 and FOS-1 in Dopaminergic Neurons
| PRJNA945491 | ENA
Project description:modENCODE_submission_3159 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP54 (official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L3; Genotype: unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene egl-5; Strain OP54 (official name : OP54 genotype : unc-119(ed3) III; wgIs54 [unc-119(+) egl-5::TY1::EGFP::3xFLAG] outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-5::EGFP fusion protein is expressed in the correct egl-5 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-5 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius
2011-03-31 | E-GEOD-25796 | biostudies-arrayexpress
Project description:To identify genes whose expression in Caenorhabditis elegans is regulated by unc-43/CamKII or egl-8/PLCbeta during adulthood, we performed an exploratory whole transcriptome RNA-sequencing (RNA-seq) study on unc-43(gf), unc-43(-), egl-8(-) and corresponding unc-43(+)/egl-8(+) control worms. To further account for potential influences of genetic background on unc-43/egl-8 function, these experiments were conducted in long-lived insulin-receptor defective [daf-2(-)], as well as in otherwise wildtype [i.e daf-2(+)] strains.
2022-10-01 | E-MTAB-11045 | biostudies-arrayexpress
Project description:modENCODE_submission_2621 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP177(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name : OP177 ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene egl-27; Strain OP177(made_by : S Kim description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The EGL-27::EGFP fusion protein is expressed in the correct egl-27 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the EGL-27 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc119(ed3);wgIs177(egl-27::TY1 EGFP FLAG;unc119) official name : OP177 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25809 | biostudies-arrayexpress
Project description:Ecotropic viral integration site 1 (EVI1/MECOM) overexpression is common in myeloid malignancies. We present a new Evi1 transgenic mouse model with inducible expression in hematopoietic stem cells (HSCs) and progenitor cells (HPCs) at lower levels. Upon exogenous Evi1 induction, mice displayed anemia, thrombocytopenia, lymphopenia, and dysplasia in erythroid and megakaryocyte cells with a significant expansion of committed myeloid progenitor cells, resembling human Myelodysplastic syndrome/Myeloproliferative neoplasm (MDS/MPN)-like disease. Methods: Lin-C-Kit+ cells were isolated from 2 Evi1 overexpressing mice for CUT&RUN assay using flag antibody and IgG. Lin-C-Kit+ cells were isolated from 2 pair of WT mice and Evi1 overexpressing mice for CUT&RUN assay using H3K27me3 antibody.Around 5X105 Lin-C-Kit+ cells for each group were used in CUT&RUN assay. About 10 ng of the purified CUT&RUN DNA was used for preparation of multiplexed libraries with the NEB Ultra II DNA Library Prep Kit per manufacturer's instruction (NEB #E7103). Sequencing was conducted using an Illumina NextSeq 500 Sequencing System. Results: Molecular pathways altered in Lin-C-Kit+ cells from Evi1-OE mice. Conclusions: Evi1 has a special binding profiling in Lin-C-Kit+ cells. The modification profile of H3K27me3 was altered in Evi1-OE hematopoietic stem and progenitor cells.
2023-06-27 | GSE235439 | GEO
Project description:Ecotropic viral integration site 1 (EVI1/MECOM) overexpression is common in myeloid malignancies. We present a new Evi1 transgenic mouse model with inducible expression in hematopoietic stem cells (HSCs) and progenitor cells (HPCs) at lower levels. Upon exogenous Evi1 induction, mice displayed anemia, thrombocytopenia, lymphopenia, and dysplasia in erythroid and megakaryocyte cells with a significant expansion of committed myeloid progenitor cells, resembling human Myelodysplastic syndrome/Myeloproliferative neoplasm (MDS/MPN)-like disease. Methods: Lin-C-Kit+ cells were isolated from 3 pairs of WT and Evi1 overexpressing mice. Around 1X106 Lin-C-Kit+ cells were harvested from each mouse. Then the cells were lysated by Trizol and total RNA was extracted by phenol-chloroform. Results: Molecular pathways altered in Lin-C-Kit+ cells from Evi1-OE mice. Conclusions: Multiple molecular pathways changed in Evi1 overexpressing hematopoietic stem and progenitor cells.
2023-06-27 | GSE235440 | GEO
Project description:Puropose: To detemine transcriptome profile of Evi1-overexpressing leukemia cells by RNA sequencing Method: RNA samples were isolated from GFP+Lin-c-kit+ mouse bone marrow cells
2020-03-31 | GSE147736 | GEO